Residual dipolar coupling

NMR residual dipolar couplings (RDCs), in the form of the projection angles between the respective internuclear bond vectors, have been used by Haliloglu et as structural restraints in the ab initio structure prediction of a test set of six proteins. The restraints have been applied using a recently developed SICHO (5/de CHain Only) lattice protein model that employs a replica exchange Monte Carlo algorithm to search conformational space. The proteins studied were ACP (77 residues), rubredoxin (53 residues), NSl, a 73 residue RNA binding/dimeriz-ation domain, Nodf (35 residues), Crd (137 residues) and Bret domain with 92 residues. 

Side-chain C-C residual dipolar couplings have been measured by Vogeli et in uniformly deuterated and enriched human ubiquitin in the presence of bacteriophages Pfl by the use of the FLOPSY family experiment, one of the many broadband polarization transfer schemes. An excellent correlation between the measured RDCs and the 3D structure of the protein has been observed, indicating a potential use of the C-C RDCs in the structure determination of perdeuterated proteins. 

It has been shown by Clore and Schwieters that the experimental Dhn 

The surface dynamics of bacteriorhodopsin has been studied by Barre et al. by solid-state NMR. They have measured site-specific H-C dipolar couplings in [3- C] Ala-labelled bacteriorhodopsin, which allowed an insight into internal fluctuation motions on the millisecond or microsecond timescale relevant to a variety of biological functions. 

More examples of proteins whose solution structure has been calculated with RDCs couplings are listed in Table 6. The corresponding data for oligonucleotides and carbohydrates are given in Table 7. 

An experiment for a simultaneous measurement of D(H, C ) and Z)(H ,C ) was proposed by Chow and Bax. The sequence is based on a 3D CB(CA)CONH experiment with the use of a quantitative approach to evaluate the coupling. Three spectra with different positions of H 180° pulse in the constant-time period are recorded in an interleaved fashion and the couplings are derived with a least-square minimisation routine. For methylene groups only the sum of /(C,H) couplings is available from the experiment. The 

Residual dipolar couplings can be used for coherence transfer in the same manner as the scalar ones. This feature was utilised in the proposed CT-COSY 

The ratio between one-bond and internucleotide dipolar couplings 

A-T basepairs. The method has high precision although the absolute value of the distance depends on the quality of the nucleotide structure used for data interpretation. 

Technological advances have provided a path to integrate the chemical diversity found in natural products in high-throughput drug discovery programmes. Many of the previous bottlenecks that made natural product discovery a slow laborious process have been effectively removed. Automation in NMR and MS has provided a path toward automated isolation of active molecules. Sensitivity improvements in NMR probe technology have allowed structures to be determined with very small quantities of material. On the other hand, 

Holcapek, L. Kolarova, K. Lemr, J. Caslavsky, P. Kacer, J. Poustka and M. Hubalek, Rapid Commun. Mass Spectrom., 2008,22, 101. 

Hopley, T. Bristow, A. Lubben, A. Simpson, E. Bull, K. Klagkou, J. Herniman and J. Langley, Rapid Commun. Mass Spectrom., 2008, 22, 1779. 

Boroczky, H. Laatsch, I. Wangner-Dobler, K. Stritzke and S. Schulz, Chem. Biodivers., 2006, 3, 622. 

MarinLit database Department of Chemistry, University of Canterbury, Christchurch, New Zealand www.chem.canterbury.ac.nz/marinlit/mar-inlit.shtml, accessed 29 April 2009. 

Gaussian axial fluctuation (GAP) model for peptide plane reorientation about the C —axis, which was initially proposed to interpret spin relaxation derived order parameters [110], is useful to describe a common anisotropic component of protein backbone dynamics [111]. A complete three-dimensional GAP (3D GAP) analysis of local motion was conducted using an extensive set of RDCs from the third immunoglobin binding domain of streptococcal protein G (GB3) [112]. The averaged coupling is calculated by using Eq. (1.39), as a function of Oy and 7, and the amph- 

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Figure 1 The principal sources of structural data are the NOEs, which give information on the spatial proximity d of protons coupling constants, which give information on dihedral angles < i and residual dipolar couplings, which give information on the relative orientation 0 of a bond vector with respect to the molecule (to the magnetic anisotropy tensor or an alignment tensor). Protons are shown as spheres. The dashed line indicates a coordinate system rigidly attached to the molecule.

A similar problem arises with present cross-validated measures of fit [92], because they also are applied to the final clean list of restraints. Residual dipolar couplings offer an entirely different and, owing to their long-range nature, very powerful way of validating structures against experimental data [93]. Similar to cross-validation, a set of residual dipolar couplings can be excluded from the refinement, and the deviations from this set are evaluated in the refined structures. 

Molecular modeling is an indispensable tool in the determination of macromolecular structures from NMR data and in the interpretation of the data. Thus, state-of-the-art molecular dynamics simulations can reproduce relaxation data well [9,96] and supply a model of the motion in atomic detail. Qualitative aspects of correlated backbone motions can be understood from NMR structure ensembles [63]. Additional data, in particular residual dipolar couplings, improve the precision and accuracy of NMR structures qualitatively [12]. 

Simon, B., Sattler, M. De novo structure determination from residual dipolar couplings by NM R spectroscopy. Angew. Chem. Int. Ed. 2002, 41, 437 40. 

Cierpicki, T., Bushweller, J. H. Charged gels as orienting media for measurement of residual dipolar couplings in soluble and integral membrane proteins. J. Am. Chem. Soc. 2004, 126, 16259-16266. 

K., Heckmann, D., Paululat, T., Kessler, H., Luy, B. Stretched poly(vinyl actetate) gels as NMR alignment media for the measurement of residual dipolar couplings in polar organic solvents. Angew. Chem. Int. Ed. 2005, 44,... 

M.)., Zartler, E. R. A Novel method for the determination of stereochemistry in six-membered chairlike rings using residual dipolar couplings. /. Org. Chem. 

Kramer, F., Deshmukh, M. V., Kessler, H., Glaser, S. J. Residual dipolar coupling constants an elementary derivation of key equations. Cone. Magn. Reson. A... 

Thiele, C. M., Berger, S. Probing the diastereotopidty of methylene protons in strychnine using residual dipolar couplings. Org. Lett. 2003, 5, 705-708. 

Kniep R, Simon P (2007) Fluorapatite-Gelatine-Nanocomposites Self-Organized Morphogenesis, Real Structure and Relations to Natural Hard Materials. 270 73-125 Koenig BW (2007) Residual Dipolar Couplings Report on the Active Conformation of Rhodopsin-Bound Protein Fragments. 272 187-216 Kolusheva S, see Jelinek R (2007) 277 155-180... 

Olejniczak ET, Meadows RP, Wang H, Cai M, Nettesheim DG, Fesik SW. Improved NMR structures of protein/ligand complexes using residual dipolar couplings. J Am Chem Soc 1999 121 9249-9250. 

Shortle has focused on the unfolded state for more than a decade, leading up to his recent demonstration using residual dipolar couplings that staphylococcal nuclease retains global structure in 8 M urea. His chapter on The Expanded Denatured State sets the stage. Dunker etal. then explore the complementary world of disordered regions within... 

Fig. 3. Scatterplots of the Nh residual dipolar couplings of A131A measured in 2, 4, 6, or 8 M urea (y-axes) plotted against the same couplings measured in the absence of urea (x-axis) ris the Pearson correlation coefficient. Alignment was achieved with alkyl PEG bicelles (Ackerman and Shortle, 2002.)...

Fig. 4. Scatterplots of the Nh residual dipolar couplings from three different denatured states of staphylococcal nuclease plotted against each other. (A) Wild-type, full-length nuclease in 4 M urea (y-axis) versus A131A in buffer (x-axis). (B) Wild-type, full-length nuclease denatured by acid (25 mM citrate, pH 3.0) (y-axis) versus A131A in buffer (x-axis).

Field cycling relaxometry Residual dipolar couplings... 

The best and easiest way to implement such an experiment is to use adiabatic inversion pulses, in order to introduce heterogeneity for evolution under 13C-1H scalar or residual dipolar couplings by means of a frequency-swept 180° pulse on 13C that inverts 13C nuclei at different positions in the NMR sample at different times (Figure 13) 40,45 This filter is robust with respect to pulse miscalibration and operates efficiently without the need to cycle the phases of pulses that otherwise is a common feature of non-destructive LPJFs. 

Other exciting applications involved using parallel tempering in connection with available experimental data. For example, Falcioni and Deem [57] used X-ray data to refine structures of zeolites, and Haliloglu et al. [58] refined NMR structural data for proteins (in particular using residual dipolar coupling constraints). 

Haliloglu, T. Kolinski, A. Skolnick, J., Use of residual dipolar couplings as restraints in ab initio protein structure prediction, Biopolymers 2003, 70, 548-562... 

Wohnert, J., Franz, K.J., Nitz, M., Imperiali, B., and Schwalbe, H. (2003) Protein alignment by a coexpressed lanthanide-binding tag for the measurement of residual dipolar couplings. J. Am. Chem. Soc. 125,13338-13339. 

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